User:Yana Fedotova/Sandbox 1

 = Photosynthesis Response Regulator PrrA of Rhodobacter sphaeroides'' =  

Background Information
 PrrA of Rhodobacter sphaeroides'' is the DNA binding protein partner of the redox-responsive two-component signal transduction regulatory system, PrrBA. PrrA regulates genes required for carbon dioxide and nitrogen fixations, photosynthesis and proton oxidation and uptake. PrrB is an integral membrane sensor histidine kinase that can phosphorylate PrrA when it senses changes in redox, such as can occur when oxygen tension change. Based on transciptome profiling, of the 4,284 genes represented in R. sphaeroides 2.4.1 GeneChip, PrrA apparently regulates 1,057.

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Structure of the Proposed PrrA Protein
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 http://ca.expasy.org/tools/protparam.html


 * This is the Amino to Carboxyl rainbow of the protein.


 * The highlighted hydrophobic regions of the protein.


 * The highlighted Glycine and Proline residues of the protein.

The PrrA protein is predicted to consist of a N-terminal receiver domain, extending from 1-130 amino acids, and a C-terminal domain covering approximately from 141-184 amino acids (residues 139-183 are ca. 90% conserved within the protein family ). It is also suggested that the C-terminal domain contains a helix-turn-helix (HTH) DNA-binding motif from 159-179 amino acids (100% conserved within the family via sequence analysis ). The two domains are said to be connected via a short proline-rich linker.

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Physico-Chemical Properties of PrrA
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Molecular weight: 20483.5 Da

Number of Amino Acids: 184

Theoretical pI: 6.85

The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). >20 hours (yeast, in vivo). >10 hours (Escherichia coli, in vivo).

Total number of negatively charged residues (Asp + Glu): 28

Total number of positively charged residues (Arg + Lys): 28

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Atomic Composition
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Carbon     C	       894 Hydrogen   H	      1468 Nitrogen   N	       268 Oxygen     O	       268 Sulfur     S	         7

Total number of atoms: 2905

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient   11585

Abs 0.1% (=1 g/l)  0.566, assuming ALL Cys residues appear as half cystines

Ext. coefficient   11460

Abs 0.1% (=1 g/l)  0.559, assuming NO Cys residues appear as half cystines

Instability index: 55.68

Aliphatic index: 95.49

Grand Average of Hydropathicity (GRAVY): -0.311

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Secondary Structure Composition of PrrA
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Alpha-helices: 34.78%

Extended (Beta-sheets): 20.65%

Other (Loops): 44.57%

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The Full-Length R. sphaeroides  PrrA Amino Acid Sequence (184 Residues)
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1 maedlvfelg adrslllvdd depflkrlak amekrgfvle taqsvaegka iaqarppaya

61 vvdlrledgn gldvvevlre rrpdcrivvl tgygaiatav aavkigatdy lskpadanev

121 thallakges lppppenpms adrvrwehiq riyemcdrnv setarrlnmh rrtlqrilak

181 rspr

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1umq
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1umq is an engineered chain structure fragment sequence of the DNA binding domain of PrrA with residues from 125 to 184 from R. sphaeroides. The cited article investigated the C-terminal effector domain of PrrA by NMR, which was said to consist of a three-helix bundle with a helix-turn-helix DNA binding motif.

http://proteopedia.org/wiki/index.php/1umq

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Phylogenetic Tree of PrrA
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http://consurf.tau.ac.il/results/1240259643/treeView.html

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Evolution of PrrA
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Amino Acid Conservation Scores

The following scores assist in examining evolutionary relatedness of the amino acid sequence of PrrA to that of other amino acid sequences.

- POS: The position of the AA in the SEQRES derived sequence.

- SEQ: The SEQRES derived sequence in one letter code.

- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.

- SCORE: The normalized conservation scores.

- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).

- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.

- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.

- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

POS	 SEQ	    		COLOR		      RESIDUE VARIETY (Normalized) 1	  D	    		  7		    	D,N,R 2	  R	    		  4		    	K,P,Q,R,Y 3	  S	    	 	  7			K,N,S,T 4	  L	    		  7			A,I,L,V 5	  L	    		  8			A,F,H,L 6	  L	    		  5			I,L,V 7	  V	    		  8			A,I,L,V 8	  D	    		  9			D,E 9	  D	    		  9			D 10	  D	    		  7			D,E,N 11	  E	    		  1			A,D,E,I,K,N,P,Q,R,S,T,V 12	  P	    	 	  3			A,D,E,G,K,L,N,P,S 13	  F	    	 	  7			F,H,I,L,T,V 14	  L	    		  6			A,C,G,L,R,S,V 15	  K	    		  1			D,E,G,H,K,N,Q,R,T,W 16	  R	    		  2			A,F,G,I,L,M,R,S,T,V,W,Y 17	  L	    		  7			F,I,L,M,T,V 18	  A	    		  2		    	A,E,G,I,N,Q,R,S,T 19	  K	    		  1			A,F,G,I,K,L,Q,R,T,V,Y 20	  A	    		  6	    		A,C,G,I,L,M,N,R,S,T 21	  M	    		  8			A,F,I,L,M 22	  E	    		  4			A,E,G,K,Q,R,S,T,V 23	  K	    		  1			A,D,E,F,G,K,L,M,Q,R,S,T 24	  R	    		  3			A,D,E,L,M,N,Q,R,S,W 25	  G	    		  9			G,K 26	  F	    		  4			F,H,L,M,Y 27	  V	    		  1			A,D,E,K,L,N,Q,R,S,T,V 28	  L	    		  7			A,C,L,P,T,V 29	  E	    		  2			A,D,E,F,H,I,K,L,R,S,T,V,Y 30	  T	    		  1			A,C,E,H,I,L,M,Q,S,T,V,W 31	  A	    		  7			A,F,H,T,V,Y 32	  Q	    		  1			A,D,E,F,G,H,N,Q,R,S,T,Y 33	  S	    		  6			D,G,H,L,N,S,T 34	  V	    		  6			A,G,L,S,T,V 35	  A	    		  1			A,D,E,H,K,L,N,P,Q,R,S,T,V 36	  E	    		  1			A,D,E,G,M,N,Q,R,S,T 37	  G	    		  7			A,F,G,L,V 38	  K	    		  2			D,E,H,I,K,L,M,R,V,W,Y 39	  A	    		  1			A,D,E,H,K,L,Q,R,T 40	  I	    		  1			A,D,E,F,G,I,K,L,M,Q,S,V,W 41	  A	    		  1			A,F,G,I,L,M,V 42	  Q	    		  1		   	A,E,H,I,K,L,M,N,P,Q,R,S,T,V 43	  A	    		  2			A,D,E,I,N,P,R,S,T 44	  R	    		  1			A,D,E,G,I,K,L,N,Q,R,V,Y 45	  P	    		  1			A,D,E,F,H,I,K,M,P,Q,R,T,V 46	  P	    		  4			A,F,G,N,P,R,V,Y 47	  A	    		  7			A,D,G,H,K,N,Q,S 48	  Y	    		  5			A,C,H,I,L,P,V,Y 49	  A	    		  5			A,C,I,L,V 50	  V	    		  4			F,I,L,V 51	  V	    		  6			C,F,I,L,M,S,T,V 52	  D	    		  9			D 53	  L	    		  6			I,L,M,V,W 54	  R	    		  7			G,K,M,N,R,T,V,W 55	  L	    		  7			L,M 56	  E	    		  7			A,D,E,G,P,S 57	  D	    		  4			D,E,G,K,N,R 58	  G	    		  5			D,E,G,I,K,L,M,T,V 59	  N	    		  7			D,N,S,T 60	  G	    		  9			A,G 61	  L	    		  6			F,I,L,M,V,W 62	  D	    		  5			A,D,E,G,H,K,Q,S 63	  V	    		  6			A,F,I,L,T,V 64	  V	    		  4			A,C,F,I,L,V 65	  E	    		  4			A,D,E,H,K,P,Q,R,Y 66	  V	    		  1			A,D,E,I,K,M,N,Q,R,T,V,Y 67	  L	    		  7			I,L,M,V,W 68	  R	    		  7			G,K,L,N,Q,R 69	  E	    		  1			A,D,E,G,I,K,Q,R,S,V 70	  R	    		  1		   	A,D,E,H,I,K,L,M,N,Q,R,S,T,V,W 71	  R	    		  1			A,D,E,G,H,K,N,Q,R,S,Y 72	  P	    		  5			A,D,I,K,L,P,Q,T,V,Y 73	  D	    		  3			A,D,E,G,H,L,M,N,Q,R,T,W 74	  C	    		  3			A,C,F,I,L,M,T,V 75	  R	    		  8			A,K,P,R 76	  I	    		  7			I,M,S,V 77	  V	    		  7			A,I,L,M,V 78	  V	    		  6			F,I,L,M,V 79	  L	    		  7			I,L,M,V 80	  T	    		  9			S,T 81	  G	    		  9			A,G,S 82	  Y	    		  7			F,H,K,L,Q,R,S,Y 83	  G	    		  6			A,D,G,N,S 84	  A	    		  5			A,D,E,N,S,T 85	  I	    		  6			E,F,I,L,V 86	  A	    		  4			A,D,E,F,I,M,P,S,T 87	  T	    		  8			A,D,E,H,L,M,N,T 88	  A	    		  9			A,E,K,R 89	  V	   		  8			I,L,V 90	  A	   		  2			A,D,E,F,I,K,L,N,Q,S 91	  A	   		  9			A,G,T 92	  V	   		  6			A,F,I,L,M,S,T,V,Y 93	  K	   		  5			A,D,E,K,N,Q,R 94	  I	   		  1		   	A,C,D,G,H,I,K,L,M,Q,R,S,T,V 95	  G	   		  9			G 96	  A	   		  9			A,S,V 97	  T	   		  5			A,D,F,L,Q,T,V,Y 98	  D	   		  9			D,E,S 99	  Y	   		  7			F,Y 100	  L	   		  7			I,L,M,V 101	  S	   		  6			A,C,E,I,P,S,T,V 102	  K	   		  9			K 103	  P	   		  9			P 104	  A	   		  7			A,C,F,L,V 105	  D	   		  7			A,D,E,G,H,N,S 106	  A	   		  4			A,D,F,I,K,L,N,P,T 107	  N	   		  6			A,D,E,G,K,N,R,T 108	  E	   		  5			A,D,E,K,N,Q,R,V 109	  V	   		  6			I,L,M,T,V 110	  T	   		  1			A,D,I,L,N,Q,R,T,V,Y 111	  H	   		  7			A,E,H,L,N,Q 112	  A	   		  8			A,L,R,S,T 113	  L	   		  5			I,L,V 114	  L	   		  4			E,H,I,K,L,Q,R 115	  A	   		  6			A,Q,R,S,T 116	  K	   		  4			A,I,K,L,N,R,V 117	  G	   		  6			G,L,S,V 118	  E	   		  8			E,R 119	  S	   		  6			A,H,R,S 120	  L	   		  6			G,L,S 121	  P	   		  4*			E,K,N,P

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Animated Image Construction
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1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html

2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.

3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.

4. On "advanced structural annotation" section select 'docking models in Capri format'.

5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.

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JMol Image Construction
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1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.

2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.

3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.

4. You can edit your protein by using the scene authoring tools after loading the applet.

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Reference
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Page Contributor
'' Yana Fedotova, email: yana.fedotova@gmail.com, yfedot@bgsu.edu

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Acknowledgments
'' Dr. Jill Zeilstra-Ryalls, Susana Retamal and Adam Meade